SIP_betaDiv_ord: Calculating & plotting beta diversity for a list of phyloseq...

In nyoungb2/HTSSIP: High Throughput Sequencing of Stable Isotope Probing Data Analysis

Description

For each phyloseq object in a list, calculates beta-diversity between all samples using the phyloseq::distance function.

Usage

SIP_betaDiv_ord(physeq_l, method = "unifrac", weighted = TRUE,
  fast = TRUE, normalized = TRUE, parallel = FALSE, plot = FALSE)

Arguments

physeq_l	A list of phyloseq objects
method	See phyloseq::distance
weighted	Weighted Unifrac (if calculating Unifrac)
fast	Fast calculation method
normalized	Normalized abundances
parallel	Calculate in parallel
plot	Return a plot (instead of a data.frame of ordination data)

Value

If plot==FALSE, a data.frame object of beta-diversity values. If plot==TRUE, a glob object for plotting.

Examples

data(physeq_S2D2_l)
## Not run: 
physeq_S2D2_l_df = SIP_betaDiv_ord(physeq_S2D2_l)
head(physeq_S2D2_l_df, n=3)

## End(Not run)

nyoungb2/HTSSIP documentation built on May 24, 2019, 11:51 a.m.